Fifteen quick tips for success with HPC, i.e., responsibly BASHing that Linux cluster
Fig 2
Parallelism in a typical HPC cluster.
The job scheduler runs on the master node and controls the highest level of parallelism in running jobs on each node (blue arrows). For example, in a variant calling pipeline, each node may perform the calling for an individual chromosome and could use multiple threads per core—3 threads per core are depicted, for a total of 12 per chromosomal job. In MPI jobs, threads on one node can communicate with threads on other nodes through inter-process communication (depicted in red dashed lines). HPC, high-performance computing; MPI, Message Passing Interface.